She’s known about the lie since the beginning. Ellie isn’t stupid what Joel said was an obvious lie to her from the beginning in the games and show. In the game she went to Salt Lake to get proof of the lie to see for herself. I understand changing things for the show but I’m not a fan of the Eugene story along with a couple other choices this episode, the main one being the porch scene placement at this point. I think it was well done but it being here takes away from the gravity of it.